AbstractWolbachia are widespread maternally-inherited bacteria, suggested to play a role in arthropod host speciation through induction of cytoplasmic incompatibility, but this hypothesis remains controversial. However, most studies focus on closely-related populations of single species, failing to consider the variable degrees of intrinsic reproductive isolation between most natural populations. Here, we dissected the interactions between Wolbachia-induced and host-associated incompatibilities in the haplodiploid spider mite Tetranychus urticae. We assessed their relative contribution to post-mating isolation between three populations of two genetically differentiated colour forms. We found that these two sources of incompatibility act through different mechanisms in an additive fashion. Host-associated incompatibility contributes 1.5 to 2 times more than Wolbachia-induced incompatibility, the former through an overproduction of haploid sons and the latter by increasing the embryonic mortality of daughters. Furthermore, regardless of cross direction, we observed near-complete hybrid sterility and complete F2 hybrid breakdown between populations of the two forms, but that Wolbachia did not contribute to this outcome. This study identifies the mechanistic independence and additive nature of these two sources of isolation, and suggests that Wolbachia could be an important driver of reproductive character displacement in this system, thereby potentially affecting host differentiation and distribution in the field.